plotCOI: Center-Of-Intensity QC Plots for Device

In xps: Processing and Analysis of Affymetrix Oligonucleotide Arrays including Exon Arrays, Whole Genome Arrays and Plate Arrays

Description

Produce Center-Of-Intensity plot(s) of the positive and negative feature intensities for the selected device.

Usage

plotCOI(x,
        type    = c("pos", "neg"),
        qualopt = "raw",
        radius  = 0.5,
        linecol = "gray70",
        visible = TRUE,
        dev     = "screen",
        outfile = "CenterOfIntensityPlot",
        w       = 540,
        h       = 540,
        ...)

Arguments

x	object of class QualTreeSet.
type	type of border elements to be used, one of “pos”, “neg”, or both.
qualopt	character string specifying whether to draw boxplots for “raw”, “adjusted”, or “normalized” border intensities.
radius	determines the radius within which the COI for each array should be located.
linecol	the color of the ablines and the circle to be drawn.
visible	logical, if TRUE then arrays outside the circle with radius will be flagged by labeling the data point with the array name.
dev	graphics device to plot to, i.e. one of “screen”, “jpeg”,“png”, “pdf” or “ps”.
outfile	the name of the output file.
w	the width of the device in pixels.
h	the height of the device in pixels.
...	optional arguments to be passed to coiplot.

Details

Produces Center-Of-Intensity (COI) plot(s) of the positive and negative feature intensities for an object of class QualTreeSet. This plot is useful for detecting spatial biases in intensities on an array.

Mean intensities for the left, right, top and bottom border elements are calculated, separated into positive and negative controls, and the “center of intensity” is calculated on a relative scale [-1,1]. Arrays with a COI outside a range with radius are considered to be outliers. If visible = TRUE then outlier arrays will be flagged by labeling the data point(s) with the array name(s).

Author(s)

Christian Stratowa

See Also

coiplot

xps documentation built on Nov. 8, 2020, 6 p.m.